Showing posts with label applied mathematics. Show all posts
Showing posts with label applied mathematics. Show all posts

1/01/2012

Applied Mathematical Models in Human Physiology (Monographs on Mathematical Modeling and Computation) Review

Applied Mathematical Models in Human Physiology (Monographs on Mathematical Modeling and Computation)
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This book is part of a series from the Society for Industrial and Applied Mathematics focusing on Mathematical Modeling and Computation. The book presents physiological and modeling fundamentals with a compilation of research in the area. It is an essential reference for anyone dealing with systems physiology modeling and downstream applications.
The content covered by chapter includes; Cardiovascular and Pulmonary Physiology and Anatomy, Blood Flow in the Heart, The Ejection Effect of the Pumping Heart, Modeling Flow and Pressure in the Systemic Arteries, A Cardiovascular Model, A Baroreceptor Model, Respiration, The SIMA Simulator, and Momentum Equation for a Small Artery.


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This book introduces mathematicians to real applications from physiology. Using mathematics to analyze physiological systems, the authors discuss models reflecting current research in cardiovascular and pulmonary physiology. In particular, they present models describing blood flow in the heart and the cardiovascular system, as well as the transport of oxygen and carbon dioxide through the respiratory system and a model for baroreceptor regulation. This is the only book available that analyzes up-to-date models of the physiological system at several levels of detail; both simple ‘real-time' models that can be directly used in larger systems, and more detailed ‘reference' models that show the underlying physiological mechanisms and provide parameters for and validation of simpler models. The book also covers two-dimensional modeling of the fluid dynamics in the heart and its ability to pump, and includes a discussion of modeling wave-propagation throughout the systemic arteries.

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12/22/2011

Process Dynamics: Modeling, Analysis and Simulation Review

Process Dynamics: Modeling, Analysis and Simulation
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This is a very clearly written book. Its contents go from easy to difficult, step by step. It's very good for beginners. For advanced readers, they may want to skip the first several chapters and read from the middle.

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Modeling, analysis and simulation of chemical processes is increasingly central to the work of chemical engineers -- but it is rarely covered in depth in process design guides. This book fills that gap. It is a comprehensive introduction to process modeling and dynamics using the powerful MATLAB and SIMULINK analysis tools.Start by understanding the rationale for process modeling, and why it is becoming so critically important. Then, review all the fundamental numerical techniques involved, including algebraic equations and numerical integration. Walk through linear systems analysis in detail, learning how to linearize non-linear models, solve linear nth Order ODE models, work with Laplace transforms and transfer function analysis, and much more. Finally, learn how to use today's increasingly-important non-linear techniques, such as phase plane analysis, quadratic maps bifurcation behavior, and analysis of chaotic behavior via Lorenz equations.For all chemical engineers, from Ph.D. professionals to non-degreed technicians and students.

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11/14/2011

Modeling Biological Systems:: Principles and Applications Review

Modeling Biological Systems:: Principles and Applications
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This book is a complete dissapointment.
It does not offer any real scientific physical models which then can be transformed in an algorithm and being simulated but is is merely a conglomerate of several statistical procedures commonly used in Biology for interpreting data (maybe copied by the author and collected from other books, as nothing that he presents is new!). This book does not offer any scientific, fundamental insight in how to really model and simulate properly complex biological systems, it is also written in a very unscientific, popular style. The mathematical level corresponds to High-School and as the author says in the preface: "The process of modeling biological systems is certainly not a science, but neither is it as unconstrained as the creation of a work of pure art that is evaluated solely on its esthetic content". I think that nonsense speaks for itself. This author should rather write novels instead of cobbling something together that gets the label "scientific" on the cover.
The book is not trash, the author does have collected some of the simplest "models" there are to describe collections of data in statistical terms, but this has NOTHING to do with proper scientific numerical and mathematical modeling and even less with scientific Computing in the field of biological complex systems, e.g. how to simulate membranes, proteins using Quantum Chemistry or Molecular dynamics techniques.
All in all I judge this book as a complete waste of money and as completely superfluous.

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This is the second edition of a textbook currently published by Springer for a course in mathematical modeling and computer simulation for biologists at the advanced undergraduate and introductory graduate level. The audience for this edition is similar to that of the previous one: advanced level courses in computational biology, as well as researchers retooling themselves. This new edition includes a CD-ROM with real examples of models as teaching tools.

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9/17/2011

Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology) Review

Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
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Regulatory networks are central to every aspect of computational biology. Determining what they are, and what genes, proteins, and post-translational modifications interact is a major and exciting field of study.
I just didn't come away from this book with that excitement. I was hoping for more about the large-scale regulation networks, but these papers go down to the quantum mechanics of interactions between pairs of molecules. I appreciate that the exact interactions matter, and that computation is probably the only way to examine some kinds of interactions (e.g. the ones in lethal mutations). It's just not what I think of as a "network."
I was also hoping for some more specifics about the computation techniques. There were some interesting insights here. For example, I never thought about the similarities between steady state chemical equilibrium and steady state Markov model behavior before, but the formalisms have striking similarities. I was also interested in some of the information-based measures for determining how well a model represents a system. I learned that the statistical assumptions behind normal chemical "equilibrium" break down at the scale of bacteria - instead, presence or absence of individual molecules matters more. Still, those were isolated kinds of facts and never came together into a whole for me.
The range of views was worthwhile. On the whole, though, the models all seemed very low-level to me, probably not well suited to handling more than a few dozen interactions, and the computation specifics were not always explicit. I'm still looking for a book with more information that I can apply directly.

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The advent of ever more sophisticated molecular manipulation techniqueshas made it clear that cellular systems are far more complex and dynamic thanpreviously thought. At the same time, experimental techniques are providing analmost overwhelming amount of new data. It is increasingly apparent that linkingmolecular and cellular structure to function will require the use of newcomputational tools.This book provides specific examples, across a wide range ofmolecular and cellular systems, of how modeling techniques can be used to explorefunctionally relevant molecular and cellular relationships. The modeling techniquescovered are applicable to cell, developmental, structural, and mathematical biology;genetics; and computational neuroscience. The book, intended as a primer for boththeoretical and experimental biologists, is organized in two parts: models of geneactivity and models of interactions among gene products. Modeling examples areprovided at several scales for each subject. Each chapter includes an overview ofthe biological system in question and extensive references to important work in thearea.

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9/01/2011

Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems (Computational Neuroscience) Review

Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems (Computational Neuroscience)
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This book is a detailed overview of the computational modeling of nervous systems from the molecular and cellular level and from the standpoint of human psychophysics and psychology. They divide their conception of modeling into descriptive, mechanistic, and interpretive models. My sole interest was in Part 3, which covers the mathematical modeling of adaptation and learning, so my review will be confined to these chapters. The virtue of this book, and others like it, is the insistence on empirical validation of the models, and not their justification by "thought experiments" and arm-chair reasoning, as is typically done in philosophy.
Part 3 begins with a discussion of synaptic plasticity and to what degree it explains learning and memory. The goal here is to develop mathematical models to understand how experience and training modify the neuronal synapses and how these changes effect the neuronal patterns and the eventual behavior. The Hebb model of neuronal firing is ubiquitous in this area of research, and the authors discuss it as a rule that synapses change in proportion to the correlation of the activities of pre- and postsynaptic neurons. Experimental data is immediately given that illustrates long-term potentiation (LTP) and long-term depression (LTD). The authors concentrate mostly on models based on unsupervised learning in this chapter. The rules for synaptic modification are given as differential equations and describe the rate of change of the synaptic weights with respect to the pre- and postsynaptic activity. The covariance and BCM rules are discussed, the first separately requiring postsynaptic and presynaptic activity, the second requiring both simultaneously. The authors consider ocular dominance in the context of unsupervised learning and study the effect of plasticity on multiple neurons. The last section of the chapter covers supervised learning, in which a set of inputs and the desired outputs are imposed during training.
In the next chapter, the authors consider the area of reinforcement learning, beginning with a discussion of the mathematical models for classical conditioning, and introducing the temporal difference learning algorithm. The authors discuss the Rescorla-Wagner rule , which is a trial-by-trial learning rule for the weight adjustments, in terms of the reward, the prediction, and the learning rate. They then discuss more realistic policies such as static action choice, where the reward/punishment immediately follows the action taken, and sequential action choice, where rewards may be delayed. The authors discuss foraging behavior of bees as an example of static action choice, reducing it to a stochastic two-armed bandit problem. The maze task for rats is discussed as an example of sequential action choice, and the authors reduce it to the "actor-critic algorithm." A generalized reinforcement learning algorithm is then discussed, with the rat water maze problem given as an example.
Chapter 10 is an overview of what the authors call "representational learning", which, as they explain, is a study of neural representations from a computational point of view. The goal is to begin with sensory input and find out how representations are generated on the basis of these inputs. That such representations are necessary is based on for example the consideration of the visual system, since, argue the authors, what is presented at the retina is too crude for an accurate representation of the visual world. The main strategy in the chapter is to begin with a deterministic or probabilistic input and construct a recognition algorithm that gives an estimate of the input. The algorithms constructed are all based on unsupervised learning, and hence the existence and nature of the causes must be computed using heuristics and the statistics of the input data. These two requirements are met via the construction of first a generative model and then a recognition model in the chapter. The familiar 'expectation maximization' is discussed as a method of optimization between real and synthetic data in generative models. A detailed overview of expectation maximization is given in the context of 'density estimation'. The authors then move on to discuss causal models for density estimation, such as Gaussian mixtures, the K-means algorithm, factor analysis, and principal components analysis. They then discuss sparse coding, as a technique to deal with the fact that the cortical activity is not Gaussian. They illustrate an experimental sample, showing the activity follows an exponential distribution in a neuron in the inferotemporal area of the macaque brain. The reader will recognize 'sparse' probability distributions as being 'heavy-tailed', i.e. having values close to zero usually, but ones far from zero sometimes. The authors emphasize the difficulties in the computation of the recognition distribution explicitly. The Olshausen/Field model is used to give a deterministic approximate recognition model for this purpose. The authors then give a fairly detailed overview of a two-layer, nonlinear 'Helmholtz machine' with binary inputs. They illustrate how to obtain the expectation maximization in terms of the Kullback-Leibler divergence. The learning in this model takes place via stochastic sampling and occurs in two phases, the so-called "wake and sleep" algorithm. The last section of the chapter gives a general discussion of how recent interest in coding, transmitting, and decoding images has led to much more research into representational learning algorithms. They discuss multi-resolution decomposition and its relationship to the coding algorithms available.

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Theoretical neuroscience provides a quantitative basis for describingwhat nervous systems do, determining how they function, and uncovering the generalprinciples by which they operate. This text introduces the basic mathematical andcomputational methods of theoretical neuroscience and presents applications in avariety of areas including vision, sensory-motor integration, development, learning,and memory.The book is divided into three parts. Part I discusses the relationshipbetween sensory stimuli and neural responses, focusing on the representation ofinformation by the spiking activity of neurons. Part II discusses the modeling ofneurons and neural circuits on the basis of cellular and synaptic biophysics. PartIII analyzes the role of plasticity in development and learning. An appendix coversthe mathematical methods used, and exercises are available on the book's Website.

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8/30/2011

Mathematics for Dynamic Modeling, Second Edition Review

Mathematics for Dynamic Modeling, Second Edition
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This is not a new cover on an older book. Having enjoyed Beltrami's first book I was glad to see a second. The new continues the subject of modeling not math. Well written, the author's book ties the conceptual difficulites of the subjects with the necessary math to get the point accross and guide the reader to new frontiers of insight again in the sense of the physical model not the math. This is a very important point! One does not lose sight of the over-all objective as with some math intensive proof types. The beauty of the work is getting the necessary across with the least. One disappointment though. The book was to short. I hope the author continues another work. Perhaps some more indepth of previous covered material. All examples and problems are easily solved in Mathcad, which already has the depth but sometimes not the explanation.

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8/13/2011

Process Dynamics, Modeling, and Control (Topics in Chemical Engineering) Review

Process Dynamics, Modeling, and Control (Topics in Chemical Engineering)
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This book was the text for my undergraduate control course. It gave me a better background in process control than the other books I purchased to supplement my learning. I highly recommend this book over others such as Marlin.
Ogunnaike and Ray covers subjects such as root locus methods, tunings using frequency methods, and digital control.
Dr. Ogunnaike is also an excellent lecturer, so if you would like to take the course directly from him enroll at the University of Delaware - its well worth it.
I also recommend Essentials of Process Control by William Luyben to provide a good qualitative background in process control.

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This text offers a modern view of process control in the context of today's technology.It provides the standard material in a coherent presentation and uses a notation that is more consistent with the research literature in process control.Topics that are unique include a unified approach to model representations, process model formation and process identification, multivariable control, statistical quality control, and model-based control.This book is designed to be used as an introductory text for undergraduate courses in process dynamics and control.In addition to chemical engineering courses, the text would also be suitable for such courses taught in mechanical, nuclear, industrial, and metallurgical engineering departments. The material is organized so that modern concepts are presented to the student but details of the most advanced material are left to later chapters.The text material has been developed, refined, and classroom tested over the last 10-15 years at the University of Wisconsin and more recently at the University of Delaware.As part of the course at Wisconsin, a laboratory has been developed to allow the students hands-on experience with measurement instruments, real time computers, and experimental process dynamics and control problems.

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